tbuckley/cabot-search huggingface dataset:
Abstract 3387: ctDNA dynamics in early stage node negative lung cancers
Authors: Jamie Feng, Tom Waddell, Kazuhiro Yasufuku, Andrew Pierre, Shaf Keshavjee, Jonathan Yeung, Marcelo Cypel, Laura Donahoe, Elliot Wakeam, Marc de Perrot, Jennifer Law, Alexandra Salvarrey, Lisa W. Le, Jennifer Lister, Michael Cabanero, Ming Tsao, Christodoulos Pipinikas, Karen Howarth, Natasha Leighl
Journal: Cancer Research (2023)

Abstract Introduction: Patients with early-stage lung cancers have a high risk of relapse and death even after curative surgery. Detection of circulating tumour DNA (ctDNA) in plasma perioperatively is associated with shorter recurrence free survival (RFS). ctDNA-Lung-Detect is an investigator-initiated prospective study of ctDNA detection and association with RFS in patients with early stage non-small cell lung cancer (NSCLC). Methods: Patients with clinically staged T&amp;lt;4cm N0 NSCLC planned for surgical resection at the Princess Margaret/University Health Network underwent ctDNA assessment before and after surgery (~1 month and 1 year). ctDNA minimal residual disease (MRD) was detected using the highly sensitive and specific tumor-informed Residual Disease and Recurrence (RaDaR®, Inivata, Cambridge, UK) assay, which can track up to 48 tumor-specific variants in plasma. Results: Since August 2021, 64 eligible patients were enrolled (Table 1). One had isolated metastasis from a remote non-lung primary and subsequently excluded; another had their preoperative sample missed but was included. Preoperative ctDNA was detected in 15/62 (23.8%) patients and 1/63 (1.6%) post-operatively at the 1-month landmark timepoint (occult N2 disease found at surgery). All but one (93.3%) had ctDNA clearance with surgical resection. Two patients have recurred radiographically and in plasma at 1 year post-operatively, 1/15 with preoperative ctDNA detected (6.7%) and 1/47 without preoperative ctDNA detected (2.1%). Patients with higher T stage, tumor size, squamous histology, and without actionable driver alterations were more likely to have ctDNA detected at any timepoint. Conclusions: In patients with early stage NSCLC (small node negative tumors), 24% have detectable ctDNA pre-operatively. Surgical resection led to ctDNA clearance in 93% of cases. Our results support ongoing testing beyond the initial MRD landmark. Assessment of the impact on RFS post resection is ongoing. Citation Format: Jamie Feng, Tom Waddell, Kazuhiro Yasufuku, Andrew Pierre, Shaf Keshavjee, Jonathan Yeung, Marcelo Cypel, Laura Donahoe, Elliot Wakeam, Marc de Perrot, Jennifer Law, Alexandra Salvarrey, Lisa W. Le, Jennifer Lister, Michael Cabanero, Ming Tsao, Christodoulos Pipinikas, Karen Howarth, Natasha Leighl. ctDNA dynamics in early stage node negative lung cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3387.
Abstract 1440: Identification of a novel EGFR sparing brain penetrant ErbB2 inhibitor with activity against oncogenic ErbB2 mutations
Authors: Mark J Chicarelli, Karyn Bouhana, Richard K. Brizendine, LouAnn Cable, Michelle Crow, Brad Fell, John Fischer, Jennifer Fulton, Anna Guarnieri, Ravi Jalluri, Hailey Knox, Keith A. Koch, Rob Rieger, John Robinson, Lee M. Stunkard, Francis Sullivan, Roy Turton, Shannon Winski, Yeyun Zhou
Journal: Cancer Research (2023)

Abstract Oncogenic driver mutations in ErbB2 (e.g., S310F/Y, L755S, V777L, V842I) are present in a variety of tumor types including gastric, uterine, urothelial carcinoma, non-small cell lung, breast, and colorectal, some of which are also known to metastasize to the CNS. These mutations can also emerge as mechanisms of acquired resistance to targeted therapies and as such represent a novel and actionable target mutation set across solid tumor indications. Current therapies that target ErbB2 have poor potency against these mutations or are limited in their utility due to inhibition of wild type epidermal growth factor receptors (WT EGFR). The inhibition of WT EGFR is associated with debilitating clinical effects that include diarrhea, stomatitis, and hepatotoxicity. Additionally, treatment of CNS metastases is especially challenging since the potential therapy must also cross the blood brain barrier to have a therapeutic effect. Next generation ErbB2 inhibitors that are active against ErbB2 mutations, spare WT EGFR, and that can penetrate the brain would provide improved target coverage with the potential for fewer off target side effects compared to current therapies and as well as the potential to exhibit superior clinical efficacy. Herein, we describe the pre-clinical in vitro and in vivo activity of a novel, brain penetrant ErbB2 inhibitor which retains potency against prevalent mutations while sparing WT EGFR. Citation Format: Mark J Chicarelli, Karyn Bouhana, Richard K. Brizendine, LouAnn Cable, Michelle Crow, Brad Fell, John Fischer, Jennifer Fulton, Anna Guarnieri, Ravi Jalluri, Hailey Knox, Keith A. Koch, Rob Rieger, John Robinson, Lee M. Stunkard, Francis Sullivan, Roy Turton, Shannon Winski, Yeyun Zhou. Identification of a novel EGFR sparing brain penetrant ErbB2 inhibitor with activity against oncogenic ErbB2 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1440.
Abstract 1339: Targeting specific extracellular matrix proteins to reactivate T cell trafficking in triple-negative breast cancer
Authors: Valentine Gauthier, Elly Tyler, Ying Liu, Tyson V. Sharp, Oliver MT Pearce
Journal: Cancer Research (2023)

Abstract It is now widely recognised that the tumour microenvironment (TME) is playing a crucial role in promoting tumour immune evasion by modulating the local immune infiltration. A growing body of evidence highlights the crucial role of the tumour extracellular matrix (ECM) in limiting trafficking of newly activated T cells in solid cancers, thus restricting their access to tumour and preventing the success of cancer immunotherapies. Accordingly, we are investigating whether targeting specific tumour ECM components may enhance T cell infiltration in triple-negative breast cancer (TNBC). Matrisome profiling of patient-derived fibroblasts and patient tumour tissues allowed us to identify two matrix proteins overexpressed in tumours and associated with T cell signatures, the matrix proteoglycan, versican (VCAN) and the glycoprotein, fibronectin (FN1). As there are currently no specific inhibitors of matrix proteins, we have modelled their loss-of-function using the clustered, regularly interspaced, short palindromic repeats-associated nuclease Cas9 (CRISPR-Cas9) technology with the goal of engineering cell-editable matrisomes which are enriched, reduced, or absent for specific matrix proteins. First, we constituted a panel of human and murine mammary fibroblast and TNBC cancer cell lines, which we have introduced with an inducible Cas9 protein expression. We measured VCAN and FN1 expression in the panel which showed distinct VCAN levels. Therefore, depending on VCAN basal levels, we have generated cell lines with VCAN overexpression, transient knockdown or stable knockout. Proteomic matrisome profiling of transient VCAN knockdown cells revealed that reducing VCAN may impact ECM abundance by decreasing VCAN direct binding partners. Finally, we used the edited cells to build 2D and 3D in vitro TME models to evaluate the impact of modulating VCAN expression on chimeric antigen receptor (CAR) T cell cytotoxicity and location. In parallel, we built in vivo mouse models of TNBC with controlled ECM deposition. Specifically, we have targeted mVcan and mFn1 in tumours and investigated the impact of their removal on tumour growth and immune cell infiltration. Overall, this work aims to identify immunomodulating features of the ECM which could be targeted to boost response to immunotherapies in solid cancers. Citation Format: Valentine Gauthier, Elly Tyler, Ying Liu, Tyson V. Sharp, Oliver MT Pearce. Targeting specific extracellular matrix proteins to reactivate T cell trafficking in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1339.
Abstract 2282: Immune modulation of the T cell repertoire in mice following immunotherapy and chemotherapy combination treatments
Authors: Yuval Elhanati, Mariam M. George, Hyejin Choi, Rachana Maniyar, Linda Hamadane, Neeman Mohibullah, Benjamin D. Greenbaum, Taha Merghoub
Journal: Cancer Research (2023)

Abstract Background: Immune checkpoint blockade therapeutics have revolutionized cancer therapy. However, most patients are either unresponsive or develop acquired resistance. Understanding patient-specific temporal T cell repertoires in the context of immune interventions will contribute to a better understanding of potential improvement strategies for better T cell anti-tumor immunity. Current methods to understand the T cell repertoire changes over time are limited due to the limited amount of material and prohibitive cost. In this study, we designed and performed longitudinal TCR sequencing in mice treated with multiple therapies. Methods: C57BL/6 mice were used in each treatment group, with blood drawn overtime before, during and after treatment. Mice were treated with a combination of immunotherapeutic agents and OVA peptide immunization, 100µl blood was drawn at multiple pre-, on- and post-treatment time points followed subsequently by TCR sequencing. Cyclophosphamide (CTX) is known to cause lymphodepletion followed by homeostatic proliferation. Thus, we also treated B16-F10 tumor bearing mice with CTX, and performed TCR sequencing on blood draws pre-, on-, and post-treatment to track TCR clone diversity and clonality over time. Results: We find that our method is sensitive enough to detect effects of immunotherapies on TCR diversity in small sample quantities. Using our method, we discovered that certain immunotherapeutic agents, most evidently CD40, have a significant but transient effect on the diversity of the T cell repertoire. We observed an initial increase in repertoire clonality, seven days post CD40 treatment followed by contraction. We show how we can identify antigen specific T cells and follow reacting T cell clones. In addition, we find that CTX treatment is associated with increased clonality in tumor bearing mice particularly in the week following treatment reflecting changes in the TCR repertoire. Conclusion: We have developed a method by which we can follow the TCR repertoire in mice treated with immunotherapy or chemotherapy. This enabled us to isolate and study the effects of different immune modulatory drugs of the endogenous T cell repertoire overtime. Citation Format: Yuval Elhanati, Mariam M. George, Hyejin Choi, Rachana Maniyar, Linda Hamadane, Neeman Mohibullah, Benjamin D. Greenbaum, Taha Merghoub. Immune modulation of the T cell repertoire in mice following immunotherapy and chemotherapy combination treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2282.
Abstract 6622: Developing spatial molecular correlates of response to immunotherapy in kidney cancer
Authors: Kathryn Beckermann, Scott Haake, Alex Nesta, Michael Caponegro, N R Nirmala, Anupama Reddy
Journal: Cancer Research (2023)

Abstract Immunotherapy has emerged as a promising new therapy for kidney cancer with durable clinical responses in a subset of the patients. However, discovery of biomarkers that predict patient response to immunotherapy has thus far been unsuccessful. Diverse sets of biomarkers have been proposed, (e.g., PD-L1 immunohistochemistry, tumor mutation burden, gene expression signatures), but have failed to validate in clinical studies. There is an urgent need to identify predictive biomarkers for selecting kidney cancer patients most likely to respond to immunotherapy. Spatial biology technologies provide molecular data at single cell resolution along with spatial coordinates in patient’s tumor slides. We hypothesized that the presence of immune cell types and their spatial 2-D patterns in a histology image could potentially predict response to immunotherapy. For this project we are using Tissue Microarray (TMAs). We are using two cohorts of data: (Dataset-1) 70 clear cell renal cell carcinoma (CCRCC) patients treated with checkpoint inhibitors, and (Dataset-2) 180 patients, early stage papillary RCC (PRCC) cohort. Dataset-1 was assayed using CosMx (Nanostring technologies) for a RNA panel of 980 immune-related genes. Dataset-2 was assayed with PhenoCycler (Akoya Biosciences) for a 31 marker protein panel with immune-related genes. We have developed methodology and novel algorithms to process both the datasets and to identify spatial phenotypes. Our pipelines include QC, normalization, dimensionality reduction and clustering. For annotation of cell types, we used as reference single cell datasets from RCC to identify tumor-type specific cell types. These cell types were mapped back to their spatial coordinates and visualized. We verified the annotations based on visual checks of their cellular morphology and organization. Next, we identified cellular neighborhoods around each cell and identified spatial clusters. We also performed a network-based analysis to identify additional spatial patterns. We performed correlation analysis with clinical phenotypes and identified spatial clusters of immune cell subtypes located in proximity of cancer cells to be associated with response to therapy. Citation Format: Kathryn Beckermann, Scott Haake, Alex Nesta, Michael Caponegro, N R Nirmala, Anupama Reddy. Developing spatial molecular correlates of response to immunotherapy in kidney cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6622.
Abstract 1535: A novel ELISA Kit:highly accuracy and sensitivity for GDF-15 detection
Authors: Meng Liang, Feng He, Meng Zhang, Yinsong Ye, Shukun Chen, Jinying Ning, Feng Hao
Journal: Cancer Research (2023)

Abstract Growth/differentiation factor 15 (GDF-15) is a promising drug target and biomarker for cancer early screening or immunotherapy. Under normal conditions, GDF-15 is expressed in low concentrations in most organs. Increased protein levels are associated with disease states such as tissue hypoxia, inflammation, acute injury and oxidative stress. The development of GDF-15 detection kit can help pharmaceutical companies in the early stage of drug development. It can also facilitate the early screening of related diseases. Hence, we developed a novel GDF-15 detected ELISA kit based on double-antibody sandwich ELISA. Our kit has ultra-high sensitivity and specificity and the concentration of GDF-15 can be detected accurately in complex biological samples such as serum, plasma or urine. First of all, mice were immunized by GDF-15. After detecting the antibody titers in sera of the immunized mice, hybridoma technologies were used to produce GDF-15 monoclonal antibodies. 57 antibodies were analyzed by epitope competition, ELISA binding and KD binding detection. The specificity of pairwise candidates was screened to obtain optimal coating and detecting antibody pair. The detecting antibody was labeled with biotin which can be conjugated with streptavidin labeled HRP. Biotin-streptavidin labeling detection method can achieve signal amplification which offers an improved detection sensitivity. Our GDF-15 detection kit has better property in sensitivity and specificity. The detection range is from 10 pg/mL to 10000 pg/mL. LOD is 5 pg/mL and LOQ is 10 pg/mL. These parameters are better than many commercial test kits. Moreover, the concentration of GDF-15 can be detected accurately in complex clinical samples. We anticipate that this GDF-15 detection kit can be applied not only for companion diagnosis, but also for related drug development. Citation Format: Meng Liang, Feng He, Meng Zhang, Yinsong Ye, Shukun Chen, Jinying Ning, Feng Hao. A novel ELISA Kit:highly accuracy and sensitivity for GDF-15 detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1535.
Abstract 5672: Comparative mouse pharmacokinetics of matched- and unmatched-isotype anti-PD-L1 antibodies
Authors: Breanna Demestichas, Sam Kleeman, Matthew Chvasta, Tobias Janowitz
Journal: Cancer Research (2023)

Abstract Immune checkpoint inhibitors (ICI) are highly effective for a minority of patients with cancer. Pre-clinical research into mechanisms of ICI resistance is reliant upon anti-PD-1 or anti-PD-L1 antibody treatment in mouse models of cancer. Common approaches utilize commercially-available rat isotype anti-PD-L1 antibodies given by intraperitoneal (IP) injection at relatively high doses (5mg/kg every 2-3 days), often for extended periods. However, there has been limited investigation into the pharmacokinetics of these antibodies with single and repeat dosing, which could inform rational dose scheduling. Non-species-matched antibodies are known to induce accelerated anti-drug immune responses, compared to species-matched antibodies. As a result, we hypothesized that matched-isotype anti-PD-L1 (based on the grafting of atezolizumab variable regions onto a mouse IgG2a scaffold) and unmatched-isotype rat IgG2b anti-PD-L1 would be associated with distinct pharmacokinetics on single and repeated dosing. We first confirmed that both matched and unmatched antibodies have nanomolar-range affinity for mouse PD-L1 by surface plasmon resonance (0.85nM and 0.37nM, respectively). Using a single IP injection in 8-week-old male C57BL/6J mice followed by repeated tail-vein plasma sampling and an indirect anti-PD-L1 ELISA, we detected a trend towards prolonged median half-life for the matched (n=17 mice) versus unmatched (n=19) antibody (91.5 versus 39.0 hours). We detected a particularly wide range of half-life measurements for matched antibody experiments (19.8 to 337.7 hours), suggesting that antibody clearance can be highly heterogeneous. Using repeated IP injection (2 doses, 14 days apart), we identified markedly accelerated antibody clearance for both antibodies resulting in comparable antibody half-lives after dose 2 (11.9 versus 12.5 hours, n=13 and n=8 mice, respectively), suggestive of a time-dependent anti-drug adaptive immune response. These findings have significant implications for in vivo antibody treatment experiments, demonstrating that repeat dosing is associated with rapid antibody clearance, irrespective of the antibody species. These data should be taken into consideration when planning longer-term antagonism of PD-1/PD-L1 signaling with antibodies in mice and strengthen the basis for short term window studies that examine the intratumoral immune biology. Furthermore, the high variability in antibody half-life suggests that antibody pharmacokinetics could confound ICI treatment response studies in vivo. Citation Format: Breanna Demestichas, Sam Kleeman, Matthew Chvasta, Tobias Janowitz. Comparative mouse pharmacokinetics of matched- and unmatched-isotype anti-PD-L1 antibodies. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5672.
Abstract 3521: CCND2 promotes proliferation in <i>Drosha</i> and <i>DICER1</i> driven tumors
Authors: Claudette R. Fraire, Uma Obalapuram, Patricia D. Tiburcio, Kavita Desai, Kenneth S. Chen
Journal: Cancer Research (2023)

Abstract Mutations in microRNA processing genes such as DROSHA and DICER1 consist of 1.5-2% of pediatric cancers including a brain tumor called pineoblastoma. We developed a genetically engineered mouse model of Drosha- and Dicer1- driven pineal tumors. These tumors develop without microRNAs and express early pineal developmental markers. Gene set enrichment analysis revealed E2F target genes to be highly expressed in these tumors. One of the most upregulated genes in these tumors is cyclin D2 (Ccnd2). Additionally, these tumors stain positively for Rb phosphorylation. In a Wilms tumor cell line (WiT49) with Drosha knocked down, RNA sequencing revealed that CCND2 was the most upregulated gene. Similarly, in patient-derived xenografts (PDXs) of DICER1-related tumors such as pleuropulmonary blastoma (PPB), we observed high expression of CCND2 and positive staining for Rb phosphorylation. To test the dependence of Rb phosphorylation in Drosha and Dicer tumors, we next treated a Drosha pineal tumor allograft with a CDK4/6 inhibitor, palbociclib, and observed tumor growth suppression. Additionally, treatment of DICER1 mutant PPB PDXs with palbociclib had similar results. These experiments suggest that CDK4/6 is important for tumor proliferation in Drosha and DICER1 driven cancers. Citation Format: Claudette R. Fraire, Uma Obalapuram, Patricia D. Tiburcio, Kavita Desai, Kenneth S. Chen. CCND2 promotes proliferation in Drosha and DICER1 driven tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3521.